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updates

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This commit is contained in:
Iliyan Angelov
2025-12-01 06:50:10 +02:00
parent 91f51bc6fe
commit 62c1fe5951
4682 changed files with 544807 additions and 31208 deletions
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83
Backend/venv/lib/python3.12/site-packages/PIL/SpiderImagePlugin.py
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@@ -32,14 +32,20 @@
# Details about the Spider image format:
# https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html
#
from __future__ import annotations
import os
import struct
import sys
from typing import IO, Any, cast
from . import Image, ImageFile
from ._util import DeferredError
TYPE_CHECKING = False
def isInt(f):
def isInt(f: Any) -> int:
try:
i = int(f)
if f - i == 0:
@@ -59,7 +65,7 @@ iforms = [1, 3, -11, -12, -21, -22]
# otherwise returns 0
def isSpiderHeader(t):
def isSpiderHeader(t: tuple[float, ...]) -> int:
h = (99,) + t # add 1 value so can use spider header index start=1
# header values 1,2,5,12,13,22,23 should be integers
for i in [1, 2, 5, 12, 13, 22, 23]:
@@ -79,7 +85,7 @@ def isSpiderHeader(t):
return labbyt
def isSpiderImage(filename):
def isSpiderImage(filename: str) -> int:
with open(filename, "rb") as fp:
f = fp.read(92) # read 23 * 4 bytes
t = struct.unpack(">23f", f) # try big-endian first
@@ -95,7 +101,7 @@ class SpiderImageFile(ImageFile.ImageFile):
format_description = "Spider 2D image"
_close_exclusive_fp_after_loading = False
def _open(self):
def _open(self) -> None:
# check header
n = 27 * 4 # read 27 float values
f = self.fp.read(n)
@@ -151,46 +157,53 @@ class SpiderImageFile(ImageFile.ImageFile):
self.rawmode = "F;32F"
self._mode = "F"
self.tile = [("raw", (0, 0) + self.size, offset, (self.rawmode, 0, 1))]
self.tile = [ImageFile._Tile("raw", (0, 0) + self.size, offset, self.rawmode)]
self._fp = self.fp # FIXME: hack
@property
def n_frames(self):
def n_frames(self) -> int:
return self._nimages
@property
def is_animated(self):
def is_animated(self) -> bool:
return self._nimages > 1
# 1st image index is zero (although SPIDER imgnumber starts at 1)
def tell(self):
def tell(self) -> int:
if self.imgnumber < 1:
return 0
else:
return self.imgnumber - 1
def seek(self, frame):
def seek(self, frame: int) -> None:
if self.istack == 0:
msg = "attempt to seek in a non-stack file"
raise EOFError(msg)
if not self._seek_check(frame):
return
if isinstance(self._fp, DeferredError):
raise self._fp.ex
self.stkoffset = self.hdrlen + frame * (self.hdrlen + self.imgbytes)
self.fp = self._fp
self.fp.seek(self.stkoffset)
self._open()
# returns a byte image after rescaling to 0..255
def convert2byte(self, depth=255):
(minimum, maximum) = self.getextrema()
m = 1
def convert2byte(self, depth: int = 255) -> Image.Image:
extrema = self.getextrema()
assert isinstance(extrema[0], float)
minimum, maximum = cast(tuple[float, float], extrema)
m: float = 1
if maximum != minimum:
m = depth / (maximum - minimum)
b = -m * minimum
return self.point(lambda i, m=m, b=b: i * m + b).convert("L")
return self.point(lambda i: i * m + b).convert("L")
if TYPE_CHECKING:
from . import ImageTk
# returns a ImageTk.PhotoImage object, after rescaling to 0..255
def tkPhotoImage(self):
def tkPhotoImage(self) -> ImageTk.PhotoImage:
from . import ImageTk
return ImageTk.PhotoImage(self.convert2byte(), palette=256)
@@ -201,33 +214,34 @@ class SpiderImageFile(ImageFile.ImageFile):
# given a list of filenames, return a list of images
def loadImageSeries(filelist=None):
def loadImageSeries(filelist: list[str] | None = None) -> list[Image.Image] | None:
"""create a list of :py:class:`~PIL.Image.Image` objects for use in a montage"""
if filelist is None or len(filelist) < 1:
return
return None
imglist = []
byte_imgs = []
for img in filelist:
if not os.path.exists(img):
print(f"unable to find {img}")
continue
try:
with Image.open(img) as im:
im = im.convert2byte()
assert isinstance(im, SpiderImageFile)
byte_im = im.convert2byte()
except Exception:
if not isSpiderImage(img):
print(img + " is not a Spider image file")
print(f"{img} is not a Spider image file")
continue
im.info["filename"] = img
imglist.append(im)
return imglist
byte_im.info["filename"] = img
byte_imgs.append(byte_im)
return byte_imgs
# --------------------------------------------------------------------
# For saving images in Spider format
def makeSpiderHeader(im):
def makeSpiderHeader(im: Image.Image) -> list[bytes]:
nsam, nrow = im.size
lenbyt = nsam * 4 # There are labrec records in the header
labrec = int(1024 / lenbyt)
@@ -238,9 +252,7 @@ def makeSpiderHeader(im):
if nvalues < 23:
return []
hdr = []
for i in range(nvalues):
hdr.append(0.0)
hdr = [0.0] * nvalues
# NB these are Fortran indices
hdr[1] = 1.0 # nslice (=1 for an image)
@@ -259,8 +271,8 @@ def makeSpiderHeader(im):
return [struct.pack("f", v) for v in hdr]
def _save(im, fp, filename):
if im.mode[0] != "F":
def _save(im: Image.Image, fp: IO[bytes], filename: str | bytes) -> None:
if im.mode != "F":
im = im.convert("F")
hdr = makeSpiderHeader(im)
@@ -272,12 +284,13 @@ def _save(im, fp, filename):
fp.writelines(hdr)
rawmode = "F;32NF" # 32-bit native floating point
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
ImageFile._save(im, fp, [ImageFile._Tile("raw", (0, 0) + im.size, 0, rawmode)])
def _save_spider(im, fp, filename):
def _save_spider(im: Image.Image, fp: IO[bytes], filename: str | bytes) -> None:
# get the filename extension and register it with Image
ext = os.path.splitext(filename)[1]
filename_ext = os.path.splitext(filename)[1]
ext = filename_ext.decode() if isinstance(filename_ext, bytes) else filename_ext
Image.register_extension(SpiderImageFile.format, ext)
_save(im, fp, filename)
@@ -299,10 +312,10 @@ if __name__ == "__main__":
sys.exit()
with Image.open(filename) as im:
print("image: " + str(im))
print("format: " + str(im.format))
print("size: " + str(im.size))
print("mode: " + str(im.mode))
print(f"image: {im}")
print(f"format: {im.format}")
print(f"size: {im.size}")
print(f"mode: {im.mode}")
print("max, min: ", end=" ")
print(im.getextrema())